Selecting Bioinformatic Tools for Public Health

Jared Johnson, PhD, MSc
April 8, 2025

Selecting Bioinformatic Tools

Expectation

Reality

Getting Started

Things to know before you start

Why do you need the tool?

  • What will be reported?

  • Who are you reporting to?

How will the tool be used?

  • Clinical vs surveillance

  • Frequency of reporting

What resources do you have?

  • Human resources (e.g., technical expertise)

  • Compute resources

  • Lab resources (e.g., sequencers)

What will be reported?

  • Bioinformatic tools often have multiple functions / outputs

  • Clearly define what will be reported (e.g., AMR genes, phylogenetic tree, clade, etc.,)

  • Helps to avoid becoming overwhelmed or distracted

Who are you reporting to?

  • Who will receive the results?

  • How will the result be used?

How will the results be used?

Clinical vs Surveillance

  • May dictate accuracy and precision requirements

Frequency of Reporting & Sample Size

  • Important when considering available resources (memory, storage, time)

What resources do you have?

Human Resources

  • Expertise and bandwidth

Compute Resources

  • Available hardware and software

  • IT restrictions

Lab Resources

  • What data can the lab produce?

Places to start

Institutions

CDC : MycoSNP, PHoeNIx, IRMA/MIRA

Broad : GATK, Terra, Cromwell, IGV, Picard, Pilon

Development Teams

Nextstrain : Nextclade, Auspice, Augur

Andersen Lab : Freyja, iVar

State Labs

UT PHL : Cecrete

WA PHL : BigBacter, VAPER, EPITOME, RECAPP, pre_mycosnp

Developers

Torsten Seemann : Prokka, Snippy, Shovill, Abricate, mlst

Ryan Wick : Unicycler, Bandage, Polypolish, Trycycler

Theiagen Genomics

github.com/Theiagen

Community Resources

Slack Channels

  • µbioinfo (microbial-bioinfo.slack.com)
  • StaPH-B (staph-b-dev.slack.com)
  • SPHERES (cspheres.slack.com)

State Public Health Bioinformatics Workgroup (StaPH-B)

  • github.com/StaPH-B/docker-builds
  • hub.docker.com/r/staphb

If all else fails…

Finding tools with AI

ChatGPT

8 tools
(no links)
(long vs short)

Copilot

3 tools
(with links)

Gemini

1 tool
(no links)

Make the Initial Selection

Tool Selection Criteria

Essential Criteria

Ideal Criteria

Don’t Fear Deadware

Deadware - software or hardware that is no longer supported, maintained, or updated by its manufacturer.

Group Activity: Downselection Criteria

Work in groups to complete the activity:

Click here

SPAdes (ChatGPT option)

Ideal Criteria

AccuVIR (Copilot option)

Ideal Criteria

VIGA (Gemini option)

Ideal Criteria

Finding Tools with AI (Round 2)

Testing the tools

Group Activity: Testing Viral Genome Assemblers

Work in groups to complete the activity:

Click here

Discussion: Testing Viral Genome Assemblers

Questions

Q1. Which assembler would you choose?


Q2. What was your big take away from the activity?


Q3. Would you add anything to the lists of “Ideal” or “Essential” criteria?